pytrax: A simple and efficient random walk implementation for calculating the directional tortuosity of images

Given the huge advances in tomographic imaging capability in recent years, image analysis has become a powerful means of measuring transport and structural properties of porous materials. One of the most important material characteristics is the tortuosity, which is difficult to measure experimentally. We present pytrax: (tortuosity from random axial movements) a simple and efficient random walk method implemented in python to calculate the average tortuosity and orthogonal directional tortuosity components of an image. The code works for both two and three-dimensional images and completes a statistically significant number of walks in parallel for large images in a few minutes using a standard desktop computer. By comparison, a Lattice Boltzmann or finite element simulation on similar sized images can take several hours

Methods for estimating the case fatality ratio for a novel, emerging infectious disease.

During the course of an epidemic of a potentially fatal disease, it is important that the case fatality ratio be well estimated. The authors propose a novel method for doing so based on the Kaplan-Meier survival procedure, jointly considering two outcomes (death and recovery), and evaluate its performance by using data from the 2003 epidemic of severe acute respiratory syndrome in Hong Kong, People's Republic of China. They compare this estimate obtained at various points in the epidemic with the case fatality ratio eventually observed; with two commonly quoted, naïve estimates derived from cumulative incidence and mortality statistics at single time points; and with estimates in which a parametric mixture model is used. They demonstrate the importance of patient characteristics regarding outcome by analyzing subgroups defined by age at admission to the hospital

Discussion: Tension stiffening in concrete beams. Part I: Fe analysis

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Community psychological and behavioral responses through the first wave of the 2009 influenza A(H1N1) pandemic in Hong Kong

Background: Little is known about the community psychological and behavioral responses to influenza pandemics. Methods: Using random digit dialing, we sampled 12,965 Hong Kong residents in 13 cross-sectional telephone surveys between April and November 2009, covering the entire first wave of the 2009 influenza A(H1N1) pandemic. We examined trends in anxiety, risk perception, knowledge on modes of transmission, and preventive behaviors. Results: Respondents reported low anxiety levels throughout the epidemic. Perceived susceptibility to infection and perceived severity of H1N1 were initially high but declined early in the epidemic and remained stable thereafter. As the epidemic grew, knowledge on modes of transmission did not improve, the adoption of hygiene measures and use of face masks did not change, and social distancing declined. Greater anxiety was associated with lower reported use of hygiene measures but greater social distancing. Knowledge that H1N1 could be spread by indirect contact was associated with greater use of hygiene measures and social distancing. Conclusions: The lack of substantial change in preventive measures or knowledge about the modes of H1N1 transmission in the general population suggests that community mitigation measures played little role in mitigating the impact of the first wave of 2009 influenza A(H1N1) pandemic in Hong Kong. © 2010 by the Infectious Diseases Society of America. All rights reserved.published_or_final_versio

Safe and complete contig assembly via omnitigs

Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs -- a set of strings that are promised to appear in any genome that could have generated the reads. From the introduction of contigs 20 years ago, assemblers have tried to obtain longer and longer contigs, but the following question was never solved: given a genome graph $G$ (e.g. a de Bruijn, or a string graph), what are all the strings that can be safely reported from $G$ as contigs? In this paper we finally answer this question, and also give a polynomial time algorithm to find them. Our experiments show that these strings, which we call omnitigs, are 66% to 82% longer on average than the popular unitigs, and 29% of dbSNP locations have more neighbors in omnitigs than in unitigs.Comment: Full version of the paper in the proceedings of RECOMB 201

Cognitive and behavioral predictors of light therapy use

Objective: Although light therapy is effective in the treatment of seasonal affective disorder (SAD) and other mood disorders, only 53-79% of individuals with SAD meet remission criteria after light therapy. Perhaps more importantly, only 12-41% of individuals with SAD continue to use the treatment even after a previous winter of successful treatment. Method: Participants completed surveys regarding (1) social, cognitive, and behavioral variables used to evaluate treatment adherence for other health-related issues, expectations and credibility of light therapy, (2) a depression symptoms scale, and (3) self-reported light therapy use. Results: Individuals age 18 or older responded (n = 40), all reporting having been diagnosed with a mood disorder for which light therapy is indicated. Social support and self-efficacy scores were predictive of light therapy use (p's<.05). Conclusion: The findings suggest that testing social support and self-efficacy in a diagnosed patient population may identify factors related to the decision to use light therapy. Treatments that impact social support and self-efficacy may improve treatment response to light therapy in SAD. © 2012 Roecklein et al

Solitary splenic metastasis from ovarian carcinosarcoma: a case report

<p>Abstract</p> <p>Introduction</p> <p>Metastatic tumors to the spleen are rare but are usually found in conjunction with metastasis to other organs. The most common sources of splenic metastasis are breast, lung and colorectal cancers as well as melanoma and ovarian carcinoma. A solitary carcinosarcoma metastasis to the spleen of any origin is very rare. To the best of our knowledge, there are fewer than 30 reported cases of ovarian primary tumors with solitary metastasis to the spleen, and only three solitary primary carcinosarcomas to the spleen have been reported, of which one is female. We present what is, to the best of our knowledge, the first case of a solitary metastatic carcinosarcoma to the spleen arising from a primary ovarian carcinsarcoma.</p> <p>Case presentation</p> <p>A 72-year-old Hispanic woman status post-total abdominal hysterectomy for ovarian carcinosarcoma presented with complaints of early satiety and abdominal pain for the past two months with a 30-lb unintentional weight loss. An initial computed tomographic scan of her abdomen and pelvis revealed a 30 cm × 27 cm splenic mass with displacement of the left kidney, stomach and liver. The patient was found to have a solitary metastatic carcinosarcoma of the spleen with biphasic epithelial (carcinomatous) and mesenchymal (sarcomatous) elements consistent with carcinosarcoma.</p> <p>Conclusion</p> <p>Carcinosarcoma of the spleen is a rare tumor. Carcinosarcomas are a biphasic neoplasm comprising malignant epithelial and mesenchymal components arising from a stem cell capable of differentiation. They can arise anywhere in the female genital tract, most commonly from the endometrium. Even though it is rare, carcinosarcomas can metastasize to the spleen. This unique case of a solitary splenic metastasis from ovarian carcinosarcoma has particular interest in medicine, especially for the specialties of surgical oncology, pathology and hematology/oncology.</p

Inverted Expression Profiles of Sex-Biased Genes in Response to Toxicant Perturbations and Diseases

10.1371/journal.pone.0056668PLoS ONE82

Changes in anti-viral effectiveness of interferon after dose reduction in chronic hepatitis c patients: a case control study

BACKGROUND: High dose interferon induction treatment of hepatitis C viral infection blocks viral production over 95%. Since dose reduction is often performed due to clinical considerations, the effect of dose reduction on hepatitis C virus kinetics was studied. METHODS: A new model that allowed longitudinal changes in the parameters of viral dynamics was used in a group of genotype-1 patients (N = 15) with dose reduction from 10 to 3 million units of interferon daily in combination with ribavirin, in comparison to a control group (N = 9) with no dose reduction. RESULTS: Dose reduction gave rise to a complex viral kinetic pattern, which could be only explained by a decrease in interferon effectiveness in blocking virion production. The benefit of the rapid initial viral decline following the high induction dose is lost after dose reduction. In addition, in some patients also the second phase viral decline slope, which is highly predictive of success of treatment, was impaired by the dose reduction resulting in smaller percentage of viral clearance in the dose reduction group. CONCLUSIONS: These findings, while explaining the failure of many induction schedules, suggest that for genotype-1 patients induction therapy should be continued till HCVRNA negativity in serum in order to increase the sustained response rate for chronic hepatitis C